Walker eating bits and a comment on the social side of research

This post has two parts: the first part presents an experiment and the second part is a comment on the social side of research today.

Part 1: walker eating bits.  In this post I introduced the walker, which has been also mentioned in the previous post.

I made several experiments with the walker, I shall start by describing the most recent one, and then I shall recall (i.e. links to posts and vids) the ones before.

I use the chemlambda gui which is available for download from here.

What I did: first I took the walker and made it walk on a trail which is generated on the fly by a pair A-FOE of nodes. I knew previously that such a pair A-FOE generates a trail of A and FO nodes, because this is the basic behaviour of the Y combinator in chemlambda. See the illustration of this (but in an older version, which uses only one type of fanout nodes, the FO) here.  Part of it was described in the pen-and-paper version in the ALIFE14 article with Louis Kauffman.

OK, if you want to see how the walker walks on the trail then you have to download first the gui and then use the gui with the file walker.mol.

Then I modified the experiment in order to feed the walker with a bit.

A bit is a pair of A-FO nodes, which has the property that it is a propagator. See here the illustration of this fact.

For this I had to modify the mol file, which I did. The new mol file is walker_eating_bit.mol .

The purpose of the experiment is to see what happens when the walker is fed with a bit. Will it preserve its shape and spill out a residue on the trail? Or will it change and degenerate to a molecule which is no longer able to walk?

The answer is shown in the following two screenshots. The first one presents the initial molecule described by the walker_eating_bit.mol.

walker_eating_bit_step0
At the extreme right you see the pair A-FOE which is generating the trail (A is the green big node with two smaller yellow ones and a small blue one and the FOE is the big yellow node with two smaller blue ones and a small yellow one). If you feel lost in the notation, then look a bit at the description in the visual tutorial.

In the middle you see the walker molecule. At the right there is the end of the trail. The walker walks from left to right, but because the trail is generated from right to left, this is seen as if the walker stays in place and the trail at its left gets longer and longer.

OK. Now, I added the bit, I said. The bit is that other pair of two green nodes, at the right of the figure, immediately at the left of the A-FOE pair from the extreme right.

The walker is going to eat this pair. What happens?

I spare you the details and I show you the result of 8 reduction steps in the next figure.

walker_eating_bit_step8

You see that the walker already passed over the bit, processed it and spat it as a pair A-FOE. Then the walker continued to walk some more steps, keeping its initial shape.

GREAT! The walker has a metabolism.

Previous experiments.  If you take the walker on the trail and you glue the ends of the trail then you get a walker tchoo-tchoo going on a circular trail. But wait, due to symmetries, this looks as a molecule which stays the same after each reduction step. Meaning this is a chemlambda quine. I called such a quine an ouroboros. In the post Quines in chemlambda you see such an ouroboros obtained from a walker which walk on a circular train track  made of only one pair.

I previously fed the walker with a node L and a termination node T, see this post for pen and paper description and this video for a more visual description, where the train track is made circular as described previously.

That’s it with the first part.

Part 2: the telling silence of the expert. The expert is no lamb in academia. He or she fiercely protect the small field of expertise where is king or queen. As you know if you read this open notebook, I have the habit of changing the research fields from time to time. This time, I entered into the the radar of artificial chemistry and graph rewriting systems, with an interest in computation. Naturally I tried to consult as many as possible experts in these fields. Here is the one and only contribution from the category theory church.  Yes, simply having a better theory does not trump racism and turf protection.  But fortunately not everything can be solved by good PR only. As it becomes more and more clear, the effect of promotion of mediocrity in academia, which was consistently followed  since the ’70, has devastating effects on the academia itself. Now we have become producers of standardised units of research, and the rest is just the monkey business about who’s on top. Gone is the the trust in science, gone are the funds, but hey, for some the establishment will still provide a good retirement.

The positive side of this big story, where I only offer concrete, punctual examples, is that the avalanche which was facilitated by the open science movement (due to the existence of the net) will change forever the academia in particular. Not into a perfect realm, because there are no such items in the real world catalogue. But the production of scientific research in the old ways of churches and you scratch my back and I’ll scratch yours is now exposed to more eyes than before and soon enough we shall witness a phenomenon similar to the one happened more than 100 years ago in art, where ossified academic art sunk into oblivion and an explosion of creativity ensued, simply because of the exposure of academic painting along with alternative (and, mixed with garbage, much more creative artists) works in the historical impressionist revolution.

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